rs11251048

Variant names:

• chr10-2078213-G-A
• rs11251048
• ENST00000435539.1:n.132-2584G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435539.1(ENSG00000226694):​n.132-2584G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,112 control chromosomes in the GnomAD database, including 6,118 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (6118 hom., cov: 33)
• Consequence: ENSG00000226694 ENST00000435539.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382

Genes affected

ENSG00000226694 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226694	ENST00000435539.1	n.132-2584G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41658 AN: 151994 Hom.: 6118 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.269

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.274 AC: 41677 AN: 152112 Hom.: 6118 Cov.: 33 AF XY: 0.271 AC XY: 20147 AN XY: 74374

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.267

Alfa AF: 0.301 Hom.: 13420

Bravo AF: 0.286

Asia WGS AF: 0.224 AC: 777 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11251048; hg19: chr10-2120407;